Multiple sequence alignment - TraesCS1A01G037300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G037300 chr1A 100.000 2786 0 0 1 2786 20890680 20887895 0.000000e+00 5145
1 TraesCS1A01G037300 chr1A 87.170 569 53 14 2186 2739 292337994 292338557 1.820000e-176 628
2 TraesCS1A01G037300 chr1B 91.634 1542 79 16 551 2062 28025586 28024065 0.000000e+00 2087
3 TraesCS1A01G037300 chr1B 89.130 322 18 9 146 463 28025894 28025586 4.350000e-103 385
4 TraesCS1A01G037300 chr1B 92.553 94 5 1 456 549 343996028 343995937 1.740000e-27 134
5 TraesCS1A01G037300 chr1B 92.553 94 5 2 459 552 354227938 354228029 1.740000e-27 134
6 TraesCS1A01G037300 chr1D 88.531 1552 99 39 545 2081 18894425 18892938 0.000000e+00 1807
7 TraesCS1A01G037300 chr1D 92.946 241 11 3 223 463 18894656 18894422 2.050000e-91 346
8 TraesCS1A01G037300 chr5B 86.969 706 76 8 1084 1776 518810094 518810796 0.000000e+00 780
9 TraesCS1A01G037300 chr5B 73.123 506 88 33 1302 1780 511852660 511853144 1.350000e-28 137
10 TraesCS1A01G037300 chr5A 86.987 707 74 10 1084 1776 545530728 545531430 0.000000e+00 780
11 TraesCS1A01G037300 chr5D 86.686 706 78 9 1084 1776 429577516 429578218 0.000000e+00 769
12 TraesCS1A01G037300 chr5D 87.246 541 65 3 2185 2724 546569528 546570065 5.100000e-172 614
13 TraesCS1A01G037300 chr5D 86.316 570 59 11 2186 2743 47328801 47329363 1.100000e-168 603
14 TraesCS1A01G037300 chr6B 87.978 549 58 6 2183 2725 251104603 251104057 2.340000e-180 641
15 TraesCS1A01G037300 chr6D 87.434 565 58 11 2191 2745 410210223 410210784 3.030000e-179 638
16 TraesCS1A01G037300 chr6D 86.865 571 59 9 2187 2747 447441744 447442308 2.360000e-175 625
17 TraesCS1A01G037300 chr7A 87.080 565 58 8 2186 2739 46281350 46280790 2.360000e-175 625
18 TraesCS1A01G037300 chr2A 87.591 548 52 12 2189 2724 755398540 755399083 3.050000e-174 621
19 TraesCS1A01G037300 chr3A 86.501 563 59 12 2186 2739 419941776 419941222 1.100000e-168 603
20 TraesCS1A01G037300 chr7D 93.478 92 4 1 459 550 195280135 195280224 4.840000e-28 135
21 TraesCS1A01G037300 chr7D 78.710 155 27 1 1305 1459 262286084 262286232 6.350000e-17 99
22 TraesCS1A01G037300 chr4B 91.919 99 5 2 457 554 661648258 661648354 4.840000e-28 135
23 TraesCS1A01G037300 chr4B 92.473 93 4 2 457 548 136939787 136939877 2.250000e-26 130
24 TraesCS1A01G037300 chr4A 93.478 92 4 1 456 547 712853622 712853533 4.840000e-28 135
25 TraesCS1A01G037300 chr7B 94.318 88 3 2 460 547 735006752 735006667 1.740000e-27 134
26 TraesCS1A01G037300 chr7B 93.333 90 4 1 459 548 388716423 388716510 6.260000e-27 132
27 TraesCS1A01G037300 chr7B 78.710 155 27 1 1305 1459 241757742 241757594 6.350000e-17 99
28 TraesCS1A01G037300 chr3D 89.524 105 7 2 453 555 554346110 554346212 2.250000e-26 130


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G037300 chr1A 20887895 20890680 2785 True 5145.0 5145 100.0000 1 2786 1 chr1A.!!$R1 2785
1 TraesCS1A01G037300 chr1A 292337994 292338557 563 False 628.0 628 87.1700 2186 2739 1 chr1A.!!$F1 553
2 TraesCS1A01G037300 chr1B 28024065 28025894 1829 True 1236.0 2087 90.3820 146 2062 2 chr1B.!!$R2 1916
3 TraesCS1A01G037300 chr1D 18892938 18894656 1718 True 1076.5 1807 90.7385 223 2081 2 chr1D.!!$R1 1858
4 TraesCS1A01G037300 chr5B 518810094 518810796 702 False 780.0 780 86.9690 1084 1776 1 chr5B.!!$F2 692
5 TraesCS1A01G037300 chr5A 545530728 545531430 702 False 780.0 780 86.9870 1084 1776 1 chr5A.!!$F1 692
6 TraesCS1A01G037300 chr5D 429577516 429578218 702 False 769.0 769 86.6860 1084 1776 1 chr5D.!!$F2 692
7 TraesCS1A01G037300 chr5D 546569528 546570065 537 False 614.0 614 87.2460 2185 2724 1 chr5D.!!$F3 539
8 TraesCS1A01G037300 chr5D 47328801 47329363 562 False 603.0 603 86.3160 2186 2743 1 chr5D.!!$F1 557
9 TraesCS1A01G037300 chr6B 251104057 251104603 546 True 641.0 641 87.9780 2183 2725 1 chr6B.!!$R1 542
10 TraesCS1A01G037300 chr6D 410210223 410210784 561 False 638.0 638 87.4340 2191 2745 1 chr6D.!!$F1 554
11 TraesCS1A01G037300 chr6D 447441744 447442308 564 False 625.0 625 86.8650 2187 2747 1 chr6D.!!$F2 560
12 TraesCS1A01G037300 chr7A 46280790 46281350 560 True 625.0 625 87.0800 2186 2739 1 chr7A.!!$R1 553
13 TraesCS1A01G037300 chr2A 755398540 755399083 543 False 621.0 621 87.5910 2189 2724 1 chr2A.!!$F1 535
14 TraesCS1A01G037300 chr3A 419941222 419941776 554 True 603.0 603 86.5010 2186 2739 1 chr3A.!!$R1 553

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
126 127 0.032515 TCGGAGGGAGAATGGCTGTA 60.033 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 2159 0.462759 GGCTACATCAGGCTGACACC 60.463 60.0 21.37 12.8 46.26 4.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.941812 CAAACAGATATCGCCCGCC 59.058 57.895 0.00 0.00 0.00 6.13
19 20 0.813610 CAAACAGATATCGCCCGCCA 60.814 55.000 0.00 0.00 0.00 5.69
20 21 0.532862 AAACAGATATCGCCCGCCAG 60.533 55.000 0.00 0.00 0.00 4.85
21 22 2.740055 CAGATATCGCCCGCCAGC 60.740 66.667 0.00 0.00 0.00 4.85
22 23 2.919856 AGATATCGCCCGCCAGCT 60.920 61.111 0.00 0.00 0.00 4.24
23 24 2.031163 GATATCGCCCGCCAGCTT 59.969 61.111 0.00 0.00 0.00 3.74
24 25 1.598130 GATATCGCCCGCCAGCTTT 60.598 57.895 0.00 0.00 0.00 3.51
25 26 1.845809 GATATCGCCCGCCAGCTTTG 61.846 60.000 0.00 0.00 0.00 2.77
26 27 2.608970 ATATCGCCCGCCAGCTTTGT 62.609 55.000 0.00 0.00 0.00 2.83
68 69 4.759205 GGCGGCCAGGGGTTTCAT 62.759 66.667 15.62 0.00 0.00 2.57
69 70 3.451894 GCGGCCAGGGGTTTCATG 61.452 66.667 2.24 0.00 0.00 3.07
75 76 3.271250 CAGGGGTTTCATGGACAGG 57.729 57.895 0.00 0.00 0.00 4.00
76 77 0.698238 CAGGGGTTTCATGGACAGGA 59.302 55.000 0.00 0.00 0.00 3.86
77 78 0.995024 AGGGGTTTCATGGACAGGAG 59.005 55.000 0.00 0.00 0.00 3.69
78 79 0.034089 GGGGTTTCATGGACAGGAGG 60.034 60.000 0.00 0.00 0.00 4.30
79 80 0.681243 GGGTTTCATGGACAGGAGGC 60.681 60.000 0.00 0.00 0.00 4.70
80 81 1.026718 GGTTTCATGGACAGGAGGCG 61.027 60.000 0.00 0.00 0.00 5.52
81 82 1.377202 TTTCATGGACAGGAGGCGC 60.377 57.895 0.00 0.00 0.00 6.53
82 83 1.841302 TTTCATGGACAGGAGGCGCT 61.841 55.000 7.64 0.00 0.00 5.92
83 84 2.202987 CATGGACAGGAGGCGCTC 60.203 66.667 7.64 2.45 0.00 5.03
84 85 2.685017 ATGGACAGGAGGCGCTCA 60.685 61.111 7.64 0.00 31.08 4.26
85 86 2.729479 ATGGACAGGAGGCGCTCAG 61.729 63.158 7.64 2.47 31.08 3.35
86 87 4.154347 GGACAGGAGGCGCTCAGG 62.154 72.222 7.64 1.73 31.08 3.86
87 88 4.154347 GACAGGAGGCGCTCAGGG 62.154 72.222 7.64 0.00 31.08 4.45
90 91 4.465446 AGGAGGCGCTCAGGGCTA 62.465 66.667 14.24 0.00 43.66 3.93
91 92 3.922640 GGAGGCGCTCAGGGCTAG 61.923 72.222 14.24 0.00 43.66 3.42
92 93 3.922640 GAGGCGCTCAGGGCTAGG 61.923 72.222 14.24 0.00 43.66 3.02
95 96 3.787001 GCGCTCAGGGCTAGGGTT 61.787 66.667 6.43 0.00 38.48 4.11
96 97 2.990479 CGCTCAGGGCTAGGGTTT 59.010 61.111 0.00 0.00 39.13 3.27
97 98 1.153349 CGCTCAGGGCTAGGGTTTC 60.153 63.158 0.00 0.00 39.13 2.78
98 99 1.899437 CGCTCAGGGCTAGGGTTTCA 61.899 60.000 0.00 0.00 39.13 2.69
99 100 0.393132 GCTCAGGGCTAGGGTTTCAC 60.393 60.000 0.00 0.00 38.06 3.18
100 101 0.253327 CTCAGGGCTAGGGTTTCACC 59.747 60.000 0.00 0.00 37.60 4.02
101 102 0.178873 TCAGGGCTAGGGTTTCACCT 60.179 55.000 0.00 0.00 44.75 4.00
102 103 0.698818 CAGGGCTAGGGTTTCACCTT 59.301 55.000 0.00 0.00 42.09 3.50
103 104 0.992695 AGGGCTAGGGTTTCACCTTC 59.007 55.000 0.00 0.00 42.09 3.46
104 105 0.696501 GGGCTAGGGTTTCACCTTCA 59.303 55.000 0.00 0.00 42.09 3.02
105 106 1.340114 GGGCTAGGGTTTCACCTTCAG 60.340 57.143 0.00 0.00 42.09 3.02
106 107 1.340114 GGCTAGGGTTTCACCTTCAGG 60.340 57.143 0.00 0.00 42.09 3.86
116 117 3.622514 CCTTCAGGTCGGAGGGAG 58.377 66.667 0.00 0.00 36.18 4.30
117 118 1.000486 CCTTCAGGTCGGAGGGAGA 60.000 63.158 0.00 0.00 36.18 3.71
118 119 0.614979 CCTTCAGGTCGGAGGGAGAA 60.615 60.000 0.00 0.00 36.18 2.87
119 120 1.490574 CTTCAGGTCGGAGGGAGAAT 58.509 55.000 0.00 0.00 0.00 2.40
120 121 1.137872 CTTCAGGTCGGAGGGAGAATG 59.862 57.143 0.00 0.00 0.00 2.67
121 122 0.687757 TCAGGTCGGAGGGAGAATGG 60.688 60.000 0.00 0.00 0.00 3.16
122 123 2.066999 AGGTCGGAGGGAGAATGGC 61.067 63.158 0.00 0.00 0.00 4.40
123 124 2.066999 GGTCGGAGGGAGAATGGCT 61.067 63.158 0.00 0.00 0.00 4.75
124 125 1.144936 GTCGGAGGGAGAATGGCTG 59.855 63.158 0.00 0.00 0.00 4.85
125 126 1.306141 TCGGAGGGAGAATGGCTGT 60.306 57.895 0.00 0.00 0.00 4.40
126 127 0.032515 TCGGAGGGAGAATGGCTGTA 60.033 55.000 0.00 0.00 0.00 2.74
127 128 1.051812 CGGAGGGAGAATGGCTGTAT 58.948 55.000 0.00 0.00 0.00 2.29
128 129 1.417890 CGGAGGGAGAATGGCTGTATT 59.582 52.381 0.00 0.00 0.00 1.89
129 130 2.158755 CGGAGGGAGAATGGCTGTATTT 60.159 50.000 0.00 0.00 0.00 1.40
130 131 3.685550 CGGAGGGAGAATGGCTGTATTTT 60.686 47.826 0.00 0.00 0.00 1.82
131 132 4.281657 GGAGGGAGAATGGCTGTATTTTT 58.718 43.478 0.00 0.00 0.00 1.94
132 133 4.339530 GGAGGGAGAATGGCTGTATTTTTC 59.660 45.833 0.00 0.00 0.00 2.29
133 134 4.934356 AGGGAGAATGGCTGTATTTTTCA 58.066 39.130 0.00 0.00 0.00 2.69
134 135 5.522641 AGGGAGAATGGCTGTATTTTTCAT 58.477 37.500 0.00 0.00 0.00 2.57
135 136 5.595952 AGGGAGAATGGCTGTATTTTTCATC 59.404 40.000 0.00 0.00 0.00 2.92
136 137 5.360714 GGGAGAATGGCTGTATTTTTCATCA 59.639 40.000 0.00 0.00 0.00 3.07
137 138 6.041296 GGGAGAATGGCTGTATTTTTCATCAT 59.959 38.462 0.00 0.00 0.00 2.45
138 139 7.231317 GGGAGAATGGCTGTATTTTTCATCATA 59.769 37.037 0.00 0.00 0.00 2.15
139 140 8.632679 GGAGAATGGCTGTATTTTTCATCATAA 58.367 33.333 0.00 0.00 0.00 1.90
173 175 2.700773 GGGGGAGTTGCATTGCGAC 61.701 63.158 19.47 19.47 42.78 5.19
179 181 1.768603 GTTGCATTGCGACTTTGCG 59.231 52.632 19.74 0.00 39.63 4.85
180 182 0.660005 GTTGCATTGCGACTTTGCGA 60.660 50.000 19.74 0.00 39.63 5.10
283 285 2.540101 CAGTTCAACCGTCACTTGACTC 59.460 50.000 7.74 0.00 42.66 3.36
284 286 2.167693 AGTTCAACCGTCACTTGACTCA 59.832 45.455 7.74 0.00 42.66 3.41
299 301 4.611310 TGACTCAAAGATAGTCGTACCG 57.389 45.455 0.00 0.00 45.19 4.02
317 319 3.000727 ACCGGTTAATCAAGCTTCTTCG 58.999 45.455 0.00 0.00 0.00 3.79
394 396 3.191371 GTGAACCAAAAAGGCAGATCGAT 59.809 43.478 0.00 0.00 43.14 3.59
396 398 3.071874 ACCAAAAAGGCAGATCGATCA 57.928 42.857 26.47 0.00 43.14 2.92
399 401 3.428045 CCAAAAAGGCAGATCGATCAACC 60.428 47.826 26.47 24.32 0.00 3.77
400 402 1.656652 AAAGGCAGATCGATCAACCG 58.343 50.000 26.47 12.90 31.56 4.44
401 403 0.824109 AAGGCAGATCGATCAACCGA 59.176 50.000 26.47 0.00 43.16 4.69
463 469 8.378421 GTGACGACATTAACTTGGTTATTACTC 58.622 37.037 0.00 0.00 0.00 2.59
464 470 7.546667 TGACGACATTAACTTGGTTATTACTCC 59.453 37.037 0.00 0.00 0.00 3.85
465 471 6.820152 ACGACATTAACTTGGTTATTACTCCC 59.180 38.462 0.00 0.00 0.00 4.30
466 472 7.046033 CGACATTAACTTGGTTATTACTCCCT 58.954 38.462 0.00 0.00 0.00 4.20
467 473 7.224167 CGACATTAACTTGGTTATTACTCCCTC 59.776 40.741 0.00 0.00 0.00 4.30
468 474 8.159229 ACATTAACTTGGTTATTACTCCCTCT 57.841 34.615 0.00 0.00 0.00 3.69
469 475 8.047310 ACATTAACTTGGTTATTACTCCCTCTG 58.953 37.037 0.00 0.00 0.00 3.35
470 476 7.563724 TTAACTTGGTTATTACTCCCTCTGT 57.436 36.000 0.00 0.00 0.00 3.41
471 477 8.669055 TTAACTTGGTTATTACTCCCTCTGTA 57.331 34.615 0.00 0.00 0.00 2.74
472 478 7.563724 AACTTGGTTATTACTCCCTCTGTAA 57.436 36.000 0.00 0.00 34.87 2.41
473 479 7.563724 ACTTGGTTATTACTCCCTCTGTAAA 57.436 36.000 0.00 0.00 34.20 2.01
474 480 7.621796 ACTTGGTTATTACTCCCTCTGTAAAG 58.378 38.462 0.00 0.00 34.20 1.85
475 481 7.237055 ACTTGGTTATTACTCCCTCTGTAAAGT 59.763 37.037 0.00 0.00 34.20 2.66
476 482 8.669055 TTGGTTATTACTCCCTCTGTAAAGTA 57.331 34.615 0.00 0.00 34.20 2.24
477 483 8.669055 TGGTTATTACTCCCTCTGTAAAGTAA 57.331 34.615 0.00 0.00 38.26 2.24
478 484 9.275572 TGGTTATTACTCCCTCTGTAAAGTAAT 57.724 33.333 10.44 10.44 43.64 1.89
487 493 9.680315 CTCCCTCTGTAAAGTAATATAAGAACG 57.320 37.037 0.00 0.00 0.00 3.95
488 494 9.193806 TCCCTCTGTAAAGTAATATAAGAACGT 57.806 33.333 0.00 0.00 0.00 3.99
489 495 9.813446 CCCTCTGTAAAGTAATATAAGAACGTT 57.187 33.333 0.00 0.00 0.00 3.99
520 526 9.733219 GATTACTAAAGTAGTGATCTAAACGCT 57.267 33.333 11.11 0.00 44.10 5.07
522 528 9.918630 TTACTAAAGTAGTGATCTAAACGCTTT 57.081 29.630 0.00 3.97 39.81 3.51
523 529 8.828688 ACTAAAGTAGTGATCTAAACGCTTTT 57.171 30.769 10.23 0.00 37.69 2.27
524 530 9.918630 ACTAAAGTAGTGATCTAAACGCTTTTA 57.081 29.630 10.23 0.00 37.69 1.52
540 546 9.977762 AAACGCTTTTATATTAGTTTACGGAAG 57.022 29.630 0.00 0.00 31.14 3.46
541 547 8.134905 ACGCTTTTATATTAGTTTACGGAAGG 57.865 34.615 0.00 0.00 0.00 3.46
542 548 7.981225 ACGCTTTTATATTAGTTTACGGAAGGA 59.019 33.333 0.00 0.00 0.00 3.36
543 549 8.485591 CGCTTTTATATTAGTTTACGGAAGGAG 58.514 37.037 0.00 0.00 0.00 3.69
544 550 9.322773 GCTTTTATATTAGTTTACGGAAGGAGT 57.677 33.333 0.00 0.00 0.00 3.85
550 556 6.655078 TTAGTTTACGGAAGGAGTACTTGT 57.345 37.500 0.00 0.00 40.21 3.16
574 580 4.562082 TGCCTTTGCTTTTTCTCATCATG 58.438 39.130 0.00 0.00 38.71 3.07
596 602 2.019948 ATGATGCATGGATCGATCGG 57.980 50.000 20.61 11.86 0.00 4.18
597 603 0.671472 TGATGCATGGATCGATCGGC 60.671 55.000 20.61 20.33 0.00 5.54
729 757 5.654317 TGTTGACACGTTCGCTTTAATAA 57.346 34.783 0.00 0.00 0.00 1.40
769 797 5.502089 TCACCTATACCCTCTCTAGCTAC 57.498 47.826 0.00 0.00 0.00 3.58
784 812 3.143211 AGCTACCTATCTACCCTGACG 57.857 52.381 0.00 0.00 0.00 4.35
802 830 3.118665 TGACGTGCCTACCTTAATTACCC 60.119 47.826 0.00 0.00 0.00 3.69
837 865 1.227380 CTCCTGCGTGCATCTACCC 60.227 63.158 0.00 0.00 0.00 3.69
842 873 0.673333 TGCGTGCATCTACCCACTTG 60.673 55.000 0.00 0.00 0.00 3.16
843 874 0.673644 GCGTGCATCTACCCACTTGT 60.674 55.000 0.00 0.00 0.00 3.16
862 893 2.667481 TGTTTTAGTATGGCACGTACGC 59.333 45.455 16.72 0.00 0.00 4.42
863 894 1.547909 TTTAGTATGGCACGTACGCG 58.452 50.000 16.72 3.53 44.93 6.01
865 896 2.970036 TAGTATGGCACGTACGCGCG 62.970 60.000 30.96 30.96 42.83 6.86
867 898 3.105852 TATGGCACGTACGCGCGTA 62.106 57.895 36.55 36.55 43.83 4.42
897 928 9.162764 ACTTTGACACGCTATAAATAAACATCT 57.837 29.630 0.00 0.00 0.00 2.90
945 980 5.119588 CAGGTGTCAATTTGCTTGCTAATTG 59.880 40.000 25.16 25.16 41.08 2.32
962 997 0.396435 TTGACCAGTGACGCTCCATT 59.604 50.000 0.00 0.00 0.00 3.16
987 1023 0.457851 ATCTCACCGGCTTCTTCTCG 59.542 55.000 0.00 0.00 0.00 4.04
997 1033 2.564553 CTTCTTCTCGGGCCGACTGG 62.565 65.000 27.46 16.41 38.77 4.00
1054 1090 2.742372 CCCTGTTTCCGCTCCACG 60.742 66.667 0.00 0.00 43.15 4.94
1057 1093 1.300620 CTGTTTCCGCTCCACGTGA 60.301 57.895 19.30 2.03 41.42 4.35
1060 1096 3.524648 TTTCCGCTCCACGTGACCC 62.525 63.158 19.30 3.09 41.42 4.46
1114 1150 0.667487 TGCGACTTCCTTCAGCTTCG 60.667 55.000 0.00 0.00 0.00 3.79
1719 1767 1.094073 ACAGCTACGCCTACGACGAT 61.094 55.000 0.00 0.00 43.93 3.73
1745 1793 2.743928 CACCTTCACCTGCTCCGC 60.744 66.667 0.00 0.00 0.00 5.54
1860 1908 4.155826 GCAGTGGACATGTATGCAGTTTAA 59.844 41.667 15.87 0.00 36.88 1.52
1965 2014 6.723052 AGGGGATTATGCTTCCTTATTCAATG 59.277 38.462 0.00 0.00 33.53 2.82
1986 2035 9.733556 TCAATGTGTATTTTGGTAATCAGTACT 57.266 29.630 0.00 0.00 32.80 2.73
2046 2095 4.379708 GCCGCCTCTTATTTTTCGGTTTAA 60.380 41.667 0.00 0.00 39.11 1.52
2066 2115 7.538678 GGTTTAATTCTTCAGCAATGTACAGTG 59.461 37.037 18.64 18.64 0.00 3.66
2073 2122 1.373570 GCAATGTACAGTGCCTCTCC 58.626 55.000 32.35 8.62 45.58 3.71
2074 2123 1.065854 GCAATGTACAGTGCCTCTCCT 60.066 52.381 32.35 0.00 45.58 3.69
2075 2124 2.898705 CAATGTACAGTGCCTCTCCTC 58.101 52.381 10.76 0.00 0.00 3.71
2076 2125 2.499289 CAATGTACAGTGCCTCTCCTCT 59.501 50.000 10.76 0.00 0.00 3.69
2077 2126 1.840737 TGTACAGTGCCTCTCCTCTC 58.159 55.000 0.00 0.00 0.00 3.20
2078 2127 1.356059 TGTACAGTGCCTCTCCTCTCT 59.644 52.381 0.00 0.00 0.00 3.10
2079 2128 2.021457 GTACAGTGCCTCTCCTCTCTC 58.979 57.143 0.00 0.00 0.00 3.20
2080 2129 0.704076 ACAGTGCCTCTCCTCTCTCT 59.296 55.000 0.00 0.00 0.00 3.10
2081 2130 1.077005 ACAGTGCCTCTCCTCTCTCTT 59.923 52.381 0.00 0.00 0.00 2.85
2082 2131 2.310349 ACAGTGCCTCTCCTCTCTCTTA 59.690 50.000 0.00 0.00 0.00 2.10
2083 2132 3.052944 ACAGTGCCTCTCCTCTCTCTTAT 60.053 47.826 0.00 0.00 0.00 1.73
2084 2133 3.960102 CAGTGCCTCTCCTCTCTCTTATT 59.040 47.826 0.00 0.00 0.00 1.40
2085 2134 4.405358 CAGTGCCTCTCCTCTCTCTTATTT 59.595 45.833 0.00 0.00 0.00 1.40
2086 2135 5.029474 AGTGCCTCTCCTCTCTCTTATTTT 58.971 41.667 0.00 0.00 0.00 1.82
2087 2136 5.487131 AGTGCCTCTCCTCTCTCTTATTTTT 59.513 40.000 0.00 0.00 0.00 1.94
2088 2137 5.815222 GTGCCTCTCCTCTCTCTTATTTTTC 59.185 44.000 0.00 0.00 0.00 2.29
2089 2138 5.485353 TGCCTCTCCTCTCTCTTATTTTTCA 59.515 40.000 0.00 0.00 0.00 2.69
2090 2139 6.157645 TGCCTCTCCTCTCTCTTATTTTTCAT 59.842 38.462 0.00 0.00 0.00 2.57
2091 2140 6.705825 GCCTCTCCTCTCTCTTATTTTTCATC 59.294 42.308 0.00 0.00 0.00 2.92
2092 2141 7.418942 GCCTCTCCTCTCTCTTATTTTTCATCT 60.419 40.741 0.00 0.00 0.00 2.90
2093 2142 9.142014 CCTCTCCTCTCTCTTATTTTTCATCTA 57.858 37.037 0.00 0.00 0.00 1.98
2105 2154 9.415544 CTTATTTTTCATCTATTATTGGCCAGC 57.584 33.333 5.11 0.00 0.00 4.85
2106 2155 5.437289 TTTTCATCTATTATTGGCCAGCG 57.563 39.130 5.11 0.00 0.00 5.18
2107 2156 2.426522 TCATCTATTATTGGCCAGCGC 58.573 47.619 5.11 0.00 0.00 5.92
2108 2157 2.038952 TCATCTATTATTGGCCAGCGCT 59.961 45.455 2.64 2.64 34.44 5.92
2109 2158 3.260632 TCATCTATTATTGGCCAGCGCTA 59.739 43.478 10.99 0.00 34.44 4.26
2110 2159 3.319137 TCTATTATTGGCCAGCGCTAG 57.681 47.619 10.99 3.03 34.44 3.42
2111 2160 2.028112 TCTATTATTGGCCAGCGCTAGG 60.028 50.000 10.99 15.68 34.44 3.02
2112 2161 0.474184 ATTATTGGCCAGCGCTAGGT 59.526 50.000 10.99 0.79 34.44 3.08
2113 2162 0.463654 TTATTGGCCAGCGCTAGGTG 60.464 55.000 10.99 0.00 44.87 4.00
2114 2163 1.622607 TATTGGCCAGCGCTAGGTGT 61.623 55.000 10.99 4.92 43.85 4.16
2115 2164 2.876368 ATTGGCCAGCGCTAGGTGTC 62.876 60.000 10.99 0.65 43.85 3.67
2116 2165 4.082523 GGCCAGCGCTAGGTGTCA 62.083 66.667 10.99 0.00 43.85 3.58
2117 2166 2.510238 GCCAGCGCTAGGTGTCAG 60.510 66.667 10.99 0.00 43.85 3.51
2118 2167 2.510238 CCAGCGCTAGGTGTCAGC 60.510 66.667 10.99 0.00 43.85 4.26
2119 2168 2.510238 CAGCGCTAGGTGTCAGCC 60.510 66.667 10.99 0.00 40.71 4.85
2120 2169 2.681778 AGCGCTAGGTGTCAGCCT 60.682 61.111 8.99 0.00 42.43 4.58
2121 2170 2.510238 GCGCTAGGTGTCAGCCTG 60.510 66.667 0.00 0.00 39.60 4.85
2122 2171 3.006756 GCGCTAGGTGTCAGCCTGA 62.007 63.158 0.00 0.00 39.60 3.86
2123 2172 1.819229 CGCTAGGTGTCAGCCTGAT 59.181 57.895 0.00 0.00 39.60 2.90
2124 2173 0.529337 CGCTAGGTGTCAGCCTGATG 60.529 60.000 0.00 0.00 39.60 3.07
2125 2174 0.539051 GCTAGGTGTCAGCCTGATGT 59.461 55.000 0.00 0.00 39.60 3.06
2126 2175 1.757118 GCTAGGTGTCAGCCTGATGTA 59.243 52.381 0.00 0.00 39.60 2.29
2127 2176 2.223923 GCTAGGTGTCAGCCTGATGTAG 60.224 54.545 0.00 0.00 39.60 2.74
2128 2177 0.539051 AGGTGTCAGCCTGATGTAGC 59.461 55.000 0.00 0.00 37.50 3.58
2129 2178 0.462759 GGTGTCAGCCTGATGTAGCC 60.463 60.000 0.00 0.00 0.00 3.93
2130 2179 0.539051 GTGTCAGCCTGATGTAGCCT 59.461 55.000 0.00 0.00 0.00 4.58
2131 2180 1.757118 GTGTCAGCCTGATGTAGCCTA 59.243 52.381 0.00 0.00 0.00 3.93
2132 2181 2.366916 GTGTCAGCCTGATGTAGCCTAT 59.633 50.000 0.00 0.00 0.00 2.57
2133 2182 3.574396 GTGTCAGCCTGATGTAGCCTATA 59.426 47.826 0.00 0.00 0.00 1.31
2134 2183 4.039245 GTGTCAGCCTGATGTAGCCTATAA 59.961 45.833 0.00 0.00 0.00 0.98
2135 2184 4.840680 TGTCAGCCTGATGTAGCCTATAAT 59.159 41.667 0.00 0.00 0.00 1.28
2136 2185 5.047021 TGTCAGCCTGATGTAGCCTATAATC 60.047 44.000 0.00 0.00 0.00 1.75
2137 2186 5.186797 GTCAGCCTGATGTAGCCTATAATCT 59.813 44.000 0.00 0.00 0.00 2.40
2138 2187 6.378564 GTCAGCCTGATGTAGCCTATAATCTA 59.621 42.308 0.00 0.00 0.00 1.98
2139 2188 7.069331 GTCAGCCTGATGTAGCCTATAATCTAT 59.931 40.741 0.00 0.00 0.00 1.98
2140 2189 8.282256 TCAGCCTGATGTAGCCTATAATCTATA 58.718 37.037 0.00 0.00 0.00 1.31
2141 2190 9.087871 CAGCCTGATGTAGCCTATAATCTATAT 57.912 37.037 0.00 0.00 0.00 0.86
2142 2191 9.308000 AGCCTGATGTAGCCTATAATCTATATC 57.692 37.037 9.09 9.09 35.38 1.63
2143 2192 9.308000 GCCTGATGTAGCCTATAATCTATATCT 57.692 37.037 13.69 0.00 35.65 1.98
2463 2532 7.362662 TCAACAGTGCATTATCTGTCTTTTTC 58.637 34.615 8.02 0.00 42.95 2.29
2492 2561 4.322424 CGGTATTGATCCGGATTGTGGATA 60.322 45.833 20.22 9.71 46.17 2.59
2496 2565 3.815809 TGATCCGGATTGTGGATAAACC 58.184 45.455 20.22 1.11 46.17 3.27
2502 2571 4.444876 CCGGATTGTGGATAAACCTCTCAT 60.445 45.833 0.00 0.00 39.86 2.90
2509 2578 8.421249 TTGTGGATAAACCTCTCATCAAAATT 57.579 30.769 0.00 0.00 39.86 1.82
2537 2606 4.253685 TGGAGACGAAATTGAAGATCACC 58.746 43.478 0.00 0.00 0.00 4.02
2538 2607 3.623510 GGAGACGAAATTGAAGATCACCC 59.376 47.826 0.00 0.00 0.00 4.61
2562 2631 6.346040 CCGCCCGTTTCTTTATACGTATTAAG 60.346 42.308 22.37 22.37 36.09 1.85
2598 2667 7.989826 AGCCATGTTTAAATAGAAGACATGTC 58.010 34.615 18.47 18.47 43.61 3.06
2629 2698 4.670896 ACTTGTGCTTTTGTAGGCAAAT 57.329 36.364 0.00 0.00 43.26 2.32
2659 2728 3.132925 TGTTTGGACCGTAGCTACAAAC 58.867 45.455 23.21 22.08 46.58 2.93
2719 2788 2.706890 TGTGGTATTCTTTTCTCCCGC 58.293 47.619 0.00 0.00 0.00 6.13
2739 2813 2.272447 GCACGGGCCCTTTTGCTAA 61.272 57.895 25.28 0.00 32.00 3.09
2743 2817 2.097036 ACGGGCCCTTTTGCTAATTAC 58.903 47.619 22.43 0.00 0.00 1.89
2744 2818 2.291346 ACGGGCCCTTTTGCTAATTACT 60.291 45.455 22.43 0.00 0.00 2.24
2746 2820 3.949113 CGGGCCCTTTTGCTAATTACTAA 59.051 43.478 22.43 0.00 0.00 2.24
2747 2821 4.583073 CGGGCCCTTTTGCTAATTACTAAT 59.417 41.667 22.43 0.00 0.00 1.73
2748 2822 5.068591 CGGGCCCTTTTGCTAATTACTAATT 59.931 40.000 22.43 0.00 34.90 1.40
2749 2823 6.263617 CGGGCCCTTTTGCTAATTACTAATTA 59.736 38.462 22.43 2.02 32.38 1.40
2750 2824 7.039993 CGGGCCCTTTTGCTAATTACTAATTAT 60.040 37.037 22.43 0.00 33.21 1.28
2751 2825 9.304335 GGGCCCTTTTGCTAATTACTAATTATA 57.696 33.333 17.04 0.00 33.21 0.98
2777 2851 7.807977 AATGAACTATGCATTATCCGTCTTT 57.192 32.000 3.54 0.00 34.41 2.52
2778 2852 7.807977 ATGAACTATGCATTATCCGTCTTTT 57.192 32.000 3.54 0.00 0.00 2.27
2779 2853 7.624360 TGAACTATGCATTATCCGTCTTTTT 57.376 32.000 3.54 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.069765 CTGGCGGGCGATATCTGTT 59.930 57.895 0.34 0.00 0.00 3.16
5 6 2.044806 AAAGCTGGCGGGCGATATCT 62.045 55.000 0.34 0.00 37.29 1.98
6 7 1.598130 AAAGCTGGCGGGCGATATC 60.598 57.895 0.00 0.00 37.29 1.63
7 8 1.893808 CAAAGCTGGCGGGCGATAT 60.894 57.895 0.00 0.00 37.29 1.63
8 9 2.513666 CAAAGCTGGCGGGCGATA 60.514 61.111 0.00 0.00 37.29 2.92
9 10 4.722700 ACAAAGCTGGCGGGCGAT 62.723 61.111 0.00 0.00 37.29 4.58
51 52 4.759205 ATGAAACCCCTGGCCGCC 62.759 66.667 1.04 1.04 0.00 6.13
52 53 3.451894 CATGAAACCCCTGGCCGC 61.452 66.667 0.00 0.00 0.00 6.53
53 54 2.755469 CCATGAAACCCCTGGCCG 60.755 66.667 0.00 0.00 0.00 6.13
54 55 1.682344 GTCCATGAAACCCCTGGCC 60.682 63.158 0.00 0.00 0.00 5.36
55 56 0.967380 CTGTCCATGAAACCCCTGGC 60.967 60.000 0.00 0.00 0.00 4.85
56 57 0.323725 CCTGTCCATGAAACCCCTGG 60.324 60.000 0.00 0.00 0.00 4.45
57 58 0.698238 TCCTGTCCATGAAACCCCTG 59.302 55.000 0.00 0.00 0.00 4.45
58 59 0.995024 CTCCTGTCCATGAAACCCCT 59.005 55.000 0.00 0.00 0.00 4.79
59 60 0.034089 CCTCCTGTCCATGAAACCCC 60.034 60.000 0.00 0.00 0.00 4.95
60 61 0.681243 GCCTCCTGTCCATGAAACCC 60.681 60.000 0.00 0.00 0.00 4.11
61 62 1.026718 CGCCTCCTGTCCATGAAACC 61.027 60.000 0.00 0.00 0.00 3.27
62 63 1.648467 GCGCCTCCTGTCCATGAAAC 61.648 60.000 0.00 0.00 0.00 2.78
63 64 1.377202 GCGCCTCCTGTCCATGAAA 60.377 57.895 0.00 0.00 0.00 2.69
64 65 2.244117 GAGCGCCTCCTGTCCATGAA 62.244 60.000 2.29 0.00 0.00 2.57
65 66 2.685017 AGCGCCTCCTGTCCATGA 60.685 61.111 2.29 0.00 0.00 3.07
66 67 2.202987 GAGCGCCTCCTGTCCATG 60.203 66.667 2.29 0.00 0.00 3.66
67 68 2.685017 TGAGCGCCTCCTGTCCAT 60.685 61.111 2.29 0.00 0.00 3.41
68 69 3.385384 CTGAGCGCCTCCTGTCCA 61.385 66.667 2.29 0.00 0.00 4.02
69 70 4.154347 CCTGAGCGCCTCCTGTCC 62.154 72.222 2.29 0.00 0.00 4.02
70 71 4.154347 CCCTGAGCGCCTCCTGTC 62.154 72.222 2.29 0.00 0.00 3.51
80 81 0.393132 GTGAAACCCTAGCCCTGAGC 60.393 60.000 0.00 0.00 44.25 4.26
81 82 3.863407 GTGAAACCCTAGCCCTGAG 57.137 57.895 0.00 0.00 0.00 3.35
99 100 0.614979 TTCTCCCTCCGACCTGAAGG 60.615 60.000 0.00 0.00 42.17 3.46
100 101 1.137872 CATTCTCCCTCCGACCTGAAG 59.862 57.143 0.00 0.00 0.00 3.02
101 102 1.195115 CATTCTCCCTCCGACCTGAA 58.805 55.000 0.00 0.00 0.00 3.02
102 103 0.687757 CCATTCTCCCTCCGACCTGA 60.688 60.000 0.00 0.00 0.00 3.86
103 104 1.826024 CCATTCTCCCTCCGACCTG 59.174 63.158 0.00 0.00 0.00 4.00
104 105 2.066999 GCCATTCTCCCTCCGACCT 61.067 63.158 0.00 0.00 0.00 3.85
105 106 2.066999 AGCCATTCTCCCTCCGACC 61.067 63.158 0.00 0.00 0.00 4.79
106 107 1.144936 CAGCCATTCTCCCTCCGAC 59.855 63.158 0.00 0.00 0.00 4.79
107 108 0.032515 TACAGCCATTCTCCCTCCGA 60.033 55.000 0.00 0.00 0.00 4.55
108 109 1.051812 ATACAGCCATTCTCCCTCCG 58.948 55.000 0.00 0.00 0.00 4.63
109 110 3.584733 AAATACAGCCATTCTCCCTCC 57.415 47.619 0.00 0.00 0.00 4.30
110 111 4.949856 TGAAAAATACAGCCATTCTCCCTC 59.050 41.667 0.00 0.00 0.00 4.30
111 112 4.934356 TGAAAAATACAGCCATTCTCCCT 58.066 39.130 0.00 0.00 0.00 4.20
112 113 5.360714 TGATGAAAAATACAGCCATTCTCCC 59.639 40.000 0.00 0.00 0.00 4.30
113 114 6.455360 TGATGAAAAATACAGCCATTCTCC 57.545 37.500 0.00 0.00 0.00 3.71
139 140 8.428852 GCAACTCCCCCAAACAATAATTATTAT 58.571 33.333 10.34 0.00 0.00 1.28
140 141 7.400339 TGCAACTCCCCCAAACAATAATTATTA 59.600 33.333 10.34 0.00 0.00 0.98
141 142 6.214412 TGCAACTCCCCCAAACAATAATTATT 59.786 34.615 4.81 4.81 0.00 1.40
142 143 5.723887 TGCAACTCCCCCAAACAATAATTAT 59.276 36.000 0.00 0.00 0.00 1.28
143 144 5.087323 TGCAACTCCCCCAAACAATAATTA 58.913 37.500 0.00 0.00 0.00 1.40
144 145 3.906846 TGCAACTCCCCCAAACAATAATT 59.093 39.130 0.00 0.00 0.00 1.40
178 180 0.597637 AGTCTTTGGCGTGTGACTCG 60.598 55.000 2.30 2.30 35.13 4.18
179 181 2.433868 TAGTCTTTGGCGTGTGACTC 57.566 50.000 0.00 0.00 39.94 3.36
180 182 2.902705 TTAGTCTTTGGCGTGTGACT 57.097 45.000 0.00 0.00 41.81 3.41
188 190 6.512297 TGATGAAAGGTTTTTAGTCTTTGGC 58.488 36.000 0.00 0.00 31.72 4.52
193 195 9.136323 AGTTGATTGATGAAAGGTTTTTAGTCT 57.864 29.630 0.00 0.00 0.00 3.24
231 233 9.320352 GAGAAAAATGCAAAAAGGGTTTTAGTA 57.680 29.630 0.00 0.00 35.12 1.82
299 301 2.747446 TGGCGAAGAAGCTTGATTAACC 59.253 45.455 2.10 4.44 37.29 2.85
334 336 2.138320 CAGATGCAATGCGGGTACTAG 58.862 52.381 0.00 0.00 0.00 2.57
364 366 2.514803 CTTTTTGGTTCACCGATCCCT 58.485 47.619 0.00 0.00 39.43 4.20
365 367 1.544246 CCTTTTTGGTTCACCGATCCC 59.456 52.381 0.00 0.00 39.43 3.85
399 401 1.522676 CATCAATTCCACCGATCGTCG 59.477 52.381 15.09 4.12 40.07 5.12
400 402 2.540101 GTCATCAATTCCACCGATCGTC 59.460 50.000 15.09 0.00 0.00 4.20
401 403 2.168521 AGTCATCAATTCCACCGATCGT 59.831 45.455 15.09 0.00 0.00 3.73
463 469 9.813446 AACGTTCTTATATTACTTTACAGAGGG 57.187 33.333 0.00 0.00 0.00 4.30
493 499 9.733219 GCGTTTAGATCACTACTTTAGTAATCT 57.267 33.333 4.72 4.72 37.23 2.40
494 500 9.733219 AGCGTTTAGATCACTACTTTAGTAATC 57.267 33.333 0.00 0.00 37.23 1.75
496 502 9.918630 AAAGCGTTTAGATCACTACTTTAGTAA 57.081 29.630 0.00 0.00 37.23 2.24
497 503 9.918630 AAAAGCGTTTAGATCACTACTTTAGTA 57.081 29.630 0.00 0.00 37.23 1.82
498 504 8.828688 AAAAGCGTTTAGATCACTACTTTAGT 57.171 30.769 0.00 0.00 40.28 2.24
514 520 9.977762 CTTCCGTAAACTAATATAAAAGCGTTT 57.022 29.630 2.53 2.53 0.00 3.60
515 521 8.606602 CCTTCCGTAAACTAATATAAAAGCGTT 58.393 33.333 0.00 0.00 0.00 4.84
516 522 7.981225 TCCTTCCGTAAACTAATATAAAAGCGT 59.019 33.333 0.00 0.00 0.00 5.07
517 523 8.356533 TCCTTCCGTAAACTAATATAAAAGCG 57.643 34.615 0.00 0.00 0.00 4.68
518 524 9.322773 ACTCCTTCCGTAAACTAATATAAAAGC 57.677 33.333 0.00 0.00 0.00 3.51
524 530 8.975295 ACAAGTACTCCTTCCGTAAACTAATAT 58.025 33.333 0.00 0.00 0.00 1.28
525 531 8.353423 ACAAGTACTCCTTCCGTAAACTAATA 57.647 34.615 0.00 0.00 0.00 0.98
526 532 7.237209 ACAAGTACTCCTTCCGTAAACTAAT 57.763 36.000 0.00 0.00 0.00 1.73
527 533 6.655078 ACAAGTACTCCTTCCGTAAACTAA 57.345 37.500 0.00 0.00 0.00 2.24
528 534 6.655078 AACAAGTACTCCTTCCGTAAACTA 57.345 37.500 0.00 0.00 0.00 2.24
529 535 5.541953 AACAAGTACTCCTTCCGTAAACT 57.458 39.130 0.00 0.00 0.00 2.66
530 536 5.559608 GCAAACAAGTACTCCTTCCGTAAAC 60.560 44.000 0.00 0.00 0.00 2.01
531 537 4.512571 GCAAACAAGTACTCCTTCCGTAAA 59.487 41.667 0.00 0.00 0.00 2.01
532 538 4.060205 GCAAACAAGTACTCCTTCCGTAA 58.940 43.478 0.00 0.00 0.00 3.18
533 539 3.555586 GGCAAACAAGTACTCCTTCCGTA 60.556 47.826 0.00 0.00 0.00 4.02
534 540 2.490991 GCAAACAAGTACTCCTTCCGT 58.509 47.619 0.00 0.00 0.00 4.69
535 541 1.804748 GGCAAACAAGTACTCCTTCCG 59.195 52.381 0.00 0.00 0.00 4.30
536 542 3.141767 AGGCAAACAAGTACTCCTTCC 57.858 47.619 0.00 0.00 0.00 3.46
537 543 4.793028 GCAAAGGCAAACAAGTACTCCTTC 60.793 45.833 10.74 0.00 40.72 3.46
538 544 3.068165 GCAAAGGCAAACAAGTACTCCTT 59.932 43.478 5.64 5.64 40.72 3.36
539 545 2.623416 GCAAAGGCAAACAAGTACTCCT 59.377 45.455 0.00 0.00 40.72 3.69
540 546 2.623416 AGCAAAGGCAAACAAGTACTCC 59.377 45.455 0.00 0.00 44.61 3.85
541 547 3.990318 AGCAAAGGCAAACAAGTACTC 57.010 42.857 0.00 0.00 44.61 2.59
542 548 4.736126 AAAGCAAAGGCAAACAAGTACT 57.264 36.364 0.00 0.00 44.61 2.73
543 549 5.580691 AGAAAAAGCAAAGGCAAACAAGTAC 59.419 36.000 0.00 0.00 44.61 2.73
544 550 5.729510 AGAAAAAGCAAAGGCAAACAAGTA 58.270 33.333 0.00 0.00 44.61 2.24
545 551 4.578871 AGAAAAAGCAAAGGCAAACAAGT 58.421 34.783 0.00 0.00 44.61 3.16
546 552 4.630940 TGAGAAAAAGCAAAGGCAAACAAG 59.369 37.500 0.00 0.00 44.61 3.16
547 553 4.573900 TGAGAAAAAGCAAAGGCAAACAA 58.426 34.783 0.00 0.00 44.61 2.83
548 554 4.199432 TGAGAAAAAGCAAAGGCAAACA 57.801 36.364 0.00 0.00 44.61 2.83
549 555 4.810491 TGATGAGAAAAAGCAAAGGCAAAC 59.190 37.500 0.00 0.00 44.61 2.93
550 556 5.021033 TGATGAGAAAAAGCAAAGGCAAA 57.979 34.783 0.00 0.00 44.61 3.68
574 580 3.739810 CCGATCGATCCATGCATCATATC 59.260 47.826 18.66 0.00 0.00 1.63
596 602 1.301009 GTGGGCTAGCTACATCGGC 60.301 63.158 15.72 0.00 0.00 5.54
597 603 1.007271 CGTGGGCTAGCTACATCGG 60.007 63.158 15.72 4.81 0.00 4.18
673 687 0.308376 TGGTAGAAAAACGTTGCCGC 59.692 50.000 0.00 0.00 37.70 6.53
729 757 3.129287 GGTGATGCGTGGATGAGAAAAAT 59.871 43.478 0.00 0.00 0.00 1.82
769 797 0.674534 GGCACGTCAGGGTAGATAGG 59.325 60.000 0.00 0.00 0.00 2.57
784 812 5.198207 ACAATGGGTAATTAAGGTAGGCAC 58.802 41.667 0.00 0.00 0.00 5.01
802 830 5.389202 CGCAGGAGATAATCGATGAACAATG 60.389 44.000 0.00 0.00 0.00 2.82
837 865 4.742438 ACGTGCCATACTAAAACAAGTG 57.258 40.909 0.00 0.00 0.00 3.16
842 873 2.284627 CGCGTACGTGCCATACTAAAAC 60.285 50.000 16.78 0.00 33.53 2.43
843 874 1.919263 CGCGTACGTGCCATACTAAAA 59.081 47.619 16.78 0.00 33.53 1.52
862 893 0.356588 CGTGTCAAAGTACGTACGCG 59.643 55.000 19.49 12.30 44.93 6.01
865 896 6.853279 TTTATAGCGTGTCAAAGTACGTAC 57.147 37.500 18.10 18.10 41.98 3.67
867 898 8.375465 GTTTATTTATAGCGTGTCAAAGTACGT 58.625 33.333 0.00 0.00 41.98 3.57
868 899 8.374728 TGTTTATTTATAGCGTGTCAAAGTACG 58.625 33.333 0.00 0.00 42.79 3.67
897 928 2.501316 TCGATCCATCTTTCTTGGCTGA 59.499 45.455 0.00 0.00 34.06 4.26
945 980 1.078759 CGAATGGAGCGTCACTGGTC 61.079 60.000 0.00 0.00 35.66 4.02
962 997 1.989966 GAAGCCGGTGAGATCGACGA 61.990 60.000 1.90 0.00 0.00 4.20
1031 1067 2.281484 GCGGAAACAGGGTGAGCA 60.281 61.111 0.00 0.00 0.00 4.26
1054 1090 2.159170 CGAGAAGGAAGATGAGGGTCAC 60.159 54.545 0.00 0.00 0.00 3.67
1057 1093 1.490574 CCGAGAAGGAAGATGAGGGT 58.509 55.000 0.00 0.00 45.00 4.34
1060 1096 0.873743 GCGCCGAGAAGGAAGATGAG 60.874 60.000 0.00 0.00 45.00 2.90
1092 1128 2.734673 GCTGAAGGAAGTCGCAGCG 61.735 63.158 9.06 9.06 43.43 5.18
1822 1870 8.506437 CATGTCCACTGCGTGATTATAATTAAT 58.494 33.333 9.75 0.00 35.23 1.40
1823 1871 7.497579 ACATGTCCACTGCGTGATTATAATTAA 59.502 33.333 9.75 0.00 35.23 1.40
1824 1872 6.989759 ACATGTCCACTGCGTGATTATAATTA 59.010 34.615 9.75 0.00 35.23 1.40
1825 1873 5.822519 ACATGTCCACTGCGTGATTATAATT 59.177 36.000 9.75 0.00 35.23 1.40
1837 1885 1.742761 ACTGCATACATGTCCACTGC 58.257 50.000 0.00 8.57 0.00 4.40
1965 2014 8.601476 GCTACAGTACTGATTACCAAAATACAC 58.399 37.037 29.30 0.00 0.00 2.90
1982 2031 5.874810 TCTCATCCATTTTGTGCTACAGTAC 59.125 40.000 0.00 0.00 0.00 2.73
1983 2032 6.048732 TCTCATCCATTTTGTGCTACAGTA 57.951 37.500 0.00 0.00 0.00 2.74
1984 2033 4.910195 TCTCATCCATTTTGTGCTACAGT 58.090 39.130 0.00 0.00 0.00 3.55
1985 2034 5.181811 TGTTCTCATCCATTTTGTGCTACAG 59.818 40.000 0.00 0.00 0.00 2.74
1986 2035 5.069318 TGTTCTCATCCATTTTGTGCTACA 58.931 37.500 0.00 0.00 0.00 2.74
2046 2095 3.441572 GGCACTGTACATTGCTGAAGAAT 59.558 43.478 29.97 0.00 37.20 2.40
2066 2115 5.983540 TGAAAAATAAGAGAGAGGAGAGGC 58.016 41.667 0.00 0.00 0.00 4.70
2067 2116 8.021898 AGATGAAAAATAAGAGAGAGGAGAGG 57.978 38.462 0.00 0.00 0.00 3.69
2079 2128 9.415544 GCTGGCCAATAATAGATGAAAAATAAG 57.584 33.333 7.01 0.00 0.00 1.73
2080 2129 8.081633 CGCTGGCCAATAATAGATGAAAAATAA 58.918 33.333 7.01 0.00 0.00 1.40
2081 2130 7.592938 CGCTGGCCAATAATAGATGAAAAATA 58.407 34.615 7.01 0.00 0.00 1.40
2082 2131 6.449698 CGCTGGCCAATAATAGATGAAAAAT 58.550 36.000 7.01 0.00 0.00 1.82
2083 2132 5.735922 GCGCTGGCCAATAATAGATGAAAAA 60.736 40.000 7.01 0.00 0.00 1.94
2084 2133 4.261572 GCGCTGGCCAATAATAGATGAAAA 60.262 41.667 7.01 0.00 0.00 2.29
2085 2134 3.253188 GCGCTGGCCAATAATAGATGAAA 59.747 43.478 7.01 0.00 0.00 2.69
2086 2135 2.813754 GCGCTGGCCAATAATAGATGAA 59.186 45.455 7.01 0.00 0.00 2.57
2087 2136 2.038952 AGCGCTGGCCAATAATAGATGA 59.961 45.455 10.39 0.00 41.24 2.92
2088 2137 2.430465 AGCGCTGGCCAATAATAGATG 58.570 47.619 10.39 0.00 41.24 2.90
2089 2138 2.867109 AGCGCTGGCCAATAATAGAT 57.133 45.000 10.39 0.00 41.24 1.98
2090 2139 2.028112 CCTAGCGCTGGCCAATAATAGA 60.028 50.000 22.90 0.00 41.24 1.98
2091 2140 2.289694 ACCTAGCGCTGGCCAATAATAG 60.290 50.000 22.90 4.68 41.24 1.73
2092 2141 1.697432 ACCTAGCGCTGGCCAATAATA 59.303 47.619 22.90 0.00 41.24 0.98
2093 2142 0.474184 ACCTAGCGCTGGCCAATAAT 59.526 50.000 22.90 0.00 41.24 1.28
2094 2143 0.463654 CACCTAGCGCTGGCCAATAA 60.464 55.000 22.90 0.00 41.24 1.40
2095 2144 1.146041 CACCTAGCGCTGGCCAATA 59.854 57.895 22.90 0.00 41.24 1.90
2096 2145 2.124570 CACCTAGCGCTGGCCAAT 60.125 61.111 22.90 0.00 41.24 3.16
2097 2146 3.605749 GACACCTAGCGCTGGCCAA 62.606 63.158 22.90 0.00 41.24 4.52
2098 2147 4.082523 GACACCTAGCGCTGGCCA 62.083 66.667 22.90 4.71 41.24 5.36
2099 2148 4.082523 TGACACCTAGCGCTGGCC 62.083 66.667 22.90 12.20 41.24 5.36
2100 2149 2.510238 CTGACACCTAGCGCTGGC 60.510 66.667 22.90 6.74 40.37 4.85
2101 2150 2.510238 GCTGACACCTAGCGCTGG 60.510 66.667 22.90 18.68 0.00 4.85
2102 2151 2.510238 GGCTGACACCTAGCGCTG 60.510 66.667 22.90 6.70 42.03 5.18
2103 2152 2.681778 AGGCTGACACCTAGCGCT 60.682 61.111 17.26 17.26 42.03 5.92
2104 2153 2.303549 ATCAGGCTGACACCTAGCGC 62.304 60.000 21.37 0.00 42.03 5.92
2105 2154 0.529337 CATCAGGCTGACACCTAGCG 60.529 60.000 21.37 0.00 42.03 4.26
2106 2155 0.539051 ACATCAGGCTGACACCTAGC 59.461 55.000 21.37 0.00 38.26 3.42
2107 2156 2.223923 GCTACATCAGGCTGACACCTAG 60.224 54.545 21.37 15.43 38.26 3.02
2108 2157 1.757118 GCTACATCAGGCTGACACCTA 59.243 52.381 21.37 5.79 38.26 3.08
2109 2158 0.539051 GCTACATCAGGCTGACACCT 59.461 55.000 21.37 0.00 42.30 4.00
2110 2159 0.462759 GGCTACATCAGGCTGACACC 60.463 60.000 21.37 12.80 46.26 4.16
2111 2160 3.071580 GGCTACATCAGGCTGACAC 57.928 57.895 21.37 7.39 46.26 3.67
2249 2300 7.973944 GCGGATTTAATTTCAGAAACATTAGGT 59.026 33.333 0.00 0.00 0.00 3.08
2253 2304 7.378181 ACTGCGGATTTAATTTCAGAAACATT 58.622 30.769 0.00 0.00 0.00 2.71
2421 2489 6.150976 CACTGTTGATTAAGATTGCACCCTAA 59.849 38.462 0.00 0.00 0.00 2.69
2492 2561 7.895429 TCCAATCCTAATTTTGATGAGAGGTTT 59.105 33.333 0.00 0.00 0.00 3.27
2496 2565 7.042187 CGTCTCCAATCCTAATTTTGATGAGAG 60.042 40.741 0.00 7.81 0.00 3.20
2502 2571 7.938140 ATTTCGTCTCCAATCCTAATTTTGA 57.062 32.000 0.00 0.00 0.00 2.69
2509 2578 6.294361 TCTTCAATTTCGTCTCCAATCCTA 57.706 37.500 0.00 0.00 0.00 2.94
2537 2606 1.643880 ACGTATAAAGAAACGGGCGG 58.356 50.000 0.00 0.00 43.25 6.13
2538 2607 6.198966 ACTTAATACGTATAAAGAAACGGGCG 59.801 38.462 8.83 0.00 43.25 6.13
2562 2631 3.855689 AAACATGGCTTGCATGTAGAC 57.144 42.857 7.39 0.00 41.85 2.59
2598 2667 5.036737 ACAAAAGCACAAGTTCAAGATTCG 58.963 37.500 0.00 0.00 0.00 3.34
2629 2698 3.495434 ACGGTCCAAACAAAGATGGTA 57.505 42.857 0.00 0.00 37.94 3.25
2698 2767 3.054361 AGCGGGAGAAAAGAATACCACAT 60.054 43.478 0.00 0.00 0.00 3.21
2719 2788 4.362476 GCAAAAGGGCCCGTGCAG 62.362 66.667 31.53 18.05 40.13 4.41
2751 2825 9.507329 AAAGACGGATAATGCATAGTTCATTAT 57.493 29.630 0.00 7.66 44.96 1.28
2752 2826 8.902540 AAAGACGGATAATGCATAGTTCATTA 57.097 30.769 0.00 0.00 39.73 1.90
2753 2827 7.807977 AAAGACGGATAATGCATAGTTCATT 57.192 32.000 0.00 0.00 37.79 2.57
2754 2828 7.807977 AAAAGACGGATAATGCATAGTTCAT 57.192 32.000 0.00 0.00 0.00 2.57
2755 2829 7.624360 AAAAAGACGGATAATGCATAGTTCA 57.376 32.000 0.00 0.00 0.00 3.18


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.